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Mendez P, Fang LT, Jablons DM, Kim IJ. Systematic comparison of two whole-genome amplification methods for targeted next-generation sequencing using frozen and FFPE normal and cancer tissues. Sci Rep 2017; 7:4055. [PMID: 28642587 PMCID: PMC5481435 DOI: 10.1038/s41598-017-04419-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 05/16/2017] [Indexed: 11/09/2022] Open
Abstract
Sequencing key cancer-driver genes using formalin-fixed, paraffin-embedded (FFPE) cancer tissues is becoming the standard for identifying the best treatment regimen. However, about 25% of all samples are rejected for genetic analyses for reasons that include too little tissue to extract enough high quality DNA. One way to overcome this is to do whole-genome amplification (WGA) in clinical samples, but only limited studies have tested different WGA methods in FFPE cancer specimens using targeted next-generation sequencing (NGS). We therefore tested the two most commonly used WGA methods, multiple displacement amplification (MDA-Qiagen REPLI-g kit) and the hybrid or modified PCR-based method (Sigma/Rubicon Genomics Inc. GenomePlex kit) in FFPE normal and tumor tissue specimens. For the normalized copy number analysis, the FFPE process caused none or very minimal bias. Variations in copy number were minimal in samples amplified using the GenomePlex kit, but they were statistically significantly higher in samples amplified using the REPLI-g kit. The pattern was similar for variant allele frequencies across the samples, which was minimal for the GenomePlex kit but highly variable for the REPLI-g kit. These findings suggest that each WGA method should be tested thoroughly before using it for clinical cancer samples.
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Affiliation(s)
- Pedro Mendez
- Thoracic Oncology Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Li Tai Fang
- Thoracic Oncology Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - David M Jablons
- Thoracic Oncology Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA.
- Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
| | - Il-Jin Kim
- Thoracic Oncology Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA.
- Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
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Premasekharan G, Gilbert E, Okimoto RA, Hamirani A, Lindquist KJ, Ngo VT, Roy R, Hough J, Edwards M, Paz R, Foye A, Sood R, Copren KA, Gubens M, Small EJ, Bivona TG, Collisson EA, Friedlander TW, Paris PL. An improved CTC isolation scheme for pairing with downstream genomics: Demonstrating clinical utility in metastatic prostate, lung and pancreatic cancer. Cancer Lett 2016; 380:144-52. [PMID: 27343980 DOI: 10.1016/j.canlet.2016.06.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 06/16/2016] [Accepted: 06/17/2016] [Indexed: 12/29/2022]
Abstract
Improvements in technologies to yield purer circulating tumor cells (CTCs) will enable a broader range of clinical applications. We have previously demonstrated the use of a commercially available cell-adhesion matrix (CAM) assay to capture invasive CTCs (iCTCs). To improve the purity of the isolated iCTCs, here we used fluorescence-activated cell sorting (FACS) in combination with the CAM assay (CAM + FACS). Our results showed an increase of median purity from the CAM assay to CAM + FACS for the spiked-in cell lines and patient samples analyzed from three different metastatic cancer types: castration resistant prostate cancer (mCRPC), non-small cell lung cancer (mNSCLC) and pancreatic ductal adenocarcinoma cancer (mPDAC). Copy number profiles for spiked-in mCRPC cell line and mCRPC patient iCTCs were similar to expected mCRPC profiles and a matched biopsy. A somatic epidermal growth factor receptor (EGFR) mutation specific to mNSCLC was observed in the iCTCs recovered from EGFR(+) mNSCLC cell lines and patient samples. Next-generation sequencing (NGS) of spiked-in pancreatic cancer cell line and mPDAC patient iCTCs showed mPDAC common mutations. CAM + FACS iCTC enrichment enables multiple downstream genomic characterizations across different tumor types.
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Affiliation(s)
- Gayatri Premasekharan
- Department of Urology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Elizabeth Gilbert
- Department of Urology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Ross A Okimoto
- Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Ashiya Hamirani
- Department of Urology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Karla J Lindquist
- Department of Urology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Vy T Ngo
- Department of Urology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Ritu Roy
- Computational Biology Core, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Jeffrey Hough
- Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Matthew Edwards
- Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Rosa Paz
- Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Adam Foye
- Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Riddhi Sood
- Genome Analysis Core, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Kirsten A Copren
- Genome Analysis Core, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Matthew Gubens
- Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Eric J Small
- Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Trever G Bivona
- Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Eric A Collisson
- Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Terence W Friedlander
- Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Pamela L Paris
- Department of Urology, University of California, San Francisco (UCSF), San Francisco, CA, USA; Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA.
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Abstract
Genetic heterogeneity explains variation in predisposition for cancer. Whole-genome analysis allows risk to be quantified, giving better targeted screening and quantification of the personalized risk posed by environmental factors. Array-based approaches to whole-genome analysis are rapidly being overtaken by next-generation sequencing (NGS). In this review the different platforms currently available for NGS are compared and the opportunities and risks of this approach are discussed: including the informatics packages required and the ethical issues. Methods applicable to the personal genome machine (PGM) are given as an example of workflows.
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Affiliation(s)
- Victoria Shaw
- NIHR Pancreatic Biomedical Research Unit, Molecular and Clinical Cancer Medicine, Royal Liverpool University Hospital, 5th Floor UCD Block, Daulby Street, Liverpool, L69 3GA, UK
| | - Katie Bullock
- NIHR Pancreatic Biomedical Research Unit, Molecular and Clinical Cancer Medicine, Royal Liverpool University Hospital, 5th Floor UCD Block, Daulby Street, Liverpool, L69 3GA, UK
| | - William Greenhalf
- NIHR Pancreatic Biomedical Research Unit, Molecular and Clinical Cancer Medicine, Royal Liverpool University Hospital, 5th Floor UCD Block, Daulby Street, Liverpool, L69 3GA, UK.
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Arneson N, Moreno J, Iakovlev V, Ghazani A, Warren K, McCready D, Jurisica I, Done SJ. Comparison of whole genome amplification methods for analysis of DNA extracted from microdissected early breast lesions in formalin-fixed paraffin-embedded tissue. ISRN ONCOLOGY 2012; 2012:710692. [PMID: 22530150 PMCID: PMC3317021 DOI: 10.5402/2012/710692] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Accepted: 11/09/2011] [Indexed: 12/03/2022]
Abstract
To understand cancer progression, it is desirable to study the earliest stages of its development, which are often microscopic lesions. Array comparative genomic hybridization (aCGH) is a valuable high-throughput molecular approach for discovering DNA copy number changes; however, it requires a relatively large amount of DNA, which is difficult to obtain from microdissected lesions. Whole genome amplification (WGA) methods were developed to increase DNA quantity; however their reproducibility, fidelity, and suitability for formalin-fixed paraffin-embedded (FFPE) samples are questioned. Using aCGH analysis, we compared two widely used approaches for WGA: single cell comparative genomic hybridization protocol (SCOMP) and degenerate oligonucleotide primed PCR (DOP-PCR). Cancer cell line and microdissected FFPE breast cancer DNA samples were amplified by the two WGA methods and subjected to aCGH. The genomic profiles of amplified DNA were compared with those of non-amplified controls by four analytic methods and validated by quantitative PCR (Q-PCR). We found that SCOMP-amplified samples had close similarity to non-amplified controls with concordance rates close to those of reference tests, while DOP-amplified samples had a statistically significant amount of changes. SCOMP is able to amplify small amounts of DNA extracted from FFPE samples and provides quality of aCGH data similar to non-amplified samples.
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Affiliation(s)
- Nona Arneson
- Division of Applied Molecular Oncology, Ontario Cancer Institute, Princess Margaret Hospital, Toronto, ON, Canada M5G 2M9
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Fiorentino M, Capizzi E, Loda M. Blood and tissue biomarkers in prostate cancer: state of the art. Urol Clin North Am 2010; 37:131-41, Table of Contents. [PMID: 20152526 DOI: 10.1016/j.ucl.2009.11.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The prevalence of prostate cancer (PCa) is high and increases with age. PCa is the most common cutaneous cancer in American men. Prostate-specific antigen (PSA) screening has impacted the detection of PCa and is directly responsible for a dramatic decrease in stage at diagnosis. Gleason score and stage at the time of diagnosis remain the mainstay to predict prognosis, in the absence of more accurate and reliable tissue or blood biomarkers. Despite extensive research efforts, very few biomarkers of PCa have been introduced to date in clinical practice. Even screening with PSA has recently been questioned. A thorough analysis of all tissue and serum biomarkers in prostate cancer research cannot be easily synthesized, and goes beyond the scope of the present article. Therefore the authors focus here on the most recently reported tissue and circulating biomarkers for PCa whose application in clinical practice is either current or expected in the near future.
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Affiliation(s)
- Michelangelo Fiorentino
- Department of Pathology and Medical Oncology, Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, D1536, 44 Binney Street, Boston, MA 02115, USA
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Lennon PA, Zhuang Y, Pierson D, Zhang X, Williams C, Perez C, Lin P. Bacterial artificial chromosome array-based comparative genomic hybridization using paired formalin-fixed, paraffin-embedded and fresh frozen tissue specimens in multiple myeloma. Cancer 2009; 115:345-54. [PMID: 19109814 DOI: 10.1002/cncr.24021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Multiple myeloma (MM) is a neoplasm of malignant plasma cells that often harbors many chromosomal aberrations. Currently, fresh frozen tissues (FT) are considered the most reliable for molecular genetic analysis; however, formalin-fixed, paraffin-embedded (FFPE) tissues are easily retrievable. Compared with conventional cytogenetics, bacterial artificial chromosome (BAC) array-comparative genomic hybridization (CGH) allows more sensitive detection of chromosomal abnormalities. METHODS The authors analyzed 7 paired FT and FFPE samples of bone marrow aspirate materials obtained from patients with MM in parallel to determine the efficacy of BAC array-CGH using FFPE. RESULTS Thirty-four aberrations were identified, including 29 that were observed in both sample types, yielding 85% concordance. Nonrandom anomalies, including gains on 7q, 9q, 15q, and 19p and losses on 8p and 13q, were observed in paired samples from at least 2 patients. To verify these results, fluorescence in situ hybridization (FISH) was performed using probes specific for 7q and 15q, and gains were observed in the 4 samples that were examined. Furthermore, 1 of 3 samples from patients who had monoclonal gammopathy of undetermined significance that were tested also carried gain on 7q, suggesting that this aberration may be an early transforming event. CONCLUSIONS The current results indicated that BAC array-CGH can be effective using FFPE samples and is a sensitive method for the identification of nonrandom chromosomal aberrations in MM.
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Affiliation(s)
- Patrick A Lennon
- School of Health Sciences, Department of Hematopathology, the University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030, USA
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Paris PL. A whole-genome amplification protocol for a wide variety of DNAs, including those from formalin-fixed and paraffin-embedded tissue. Methods Mol Biol 2009; 556:89-98. [PMID: 19488873 DOI: 10.1007/978-1-60327-192-9_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Abstract
High-resolution genomic arrays and next-generation sequencers are some of the genome-based technologies poised to make significant contributions in the near future to basic and clinical science. The success of these technologies, and most certainly their translation into the clinic, will require that they produce high quality, reproducible data from small archived tumor specimens, including biopsies. DNA from patient samples, especially archival tissue, can be a limiting factor and lead to the need for amplification of the starting material. A variety of whole-genome amplification techniques are available, but choosing the most reliable, reproducible amplification technology that will be suitable for use across a wide spectrum of clinical specimens is essential. Sigma's whole-genome amplification kit provides a robust, highly reliable, and versatile amplification system across a variety of DNA sources. This chapter will detail Sigma's amplification protocol along with an optimized DNA extraction protocol for formalin-fixed and paraffin-embedded tissue.
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Affiliation(s)
- Pamela L Paris
- Department of Urology, University of California at San Francisco, San Francisco, CA, USA
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